PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2Q7G
Biol. Unit 1
Info
Asym.Unit (57 KB)
Biol.Unit 1 (99 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PYRROLYSINE TRNA SYNTHETASE BOUND TO A PYRROLYSINE ANALOGUE (CYC) AND ATP
Authors
:
J. M. Kavran, T. A. Steitz
Date
:
06 Jun 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Pyrrolysyl-Trna Syntethetase, Pyrrolysine, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Kavran, S. Gundllapalli, P. O'Donoghue, M. Englert, D. Soll, T. A. Steitz
Structure Of Pyrrolysyl-Trna Synthetase, An Archaeal Enzyme For Genetic Code Innovation.
Proc. Natl. Acad. Sci. Usa V. 104 11268 2007
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: N~6~-[(CYCLOPENTYLOXY)CARBONYL]-D-... (CCLa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CCL
2
Ligand/Ion
N~6~-[(CYCLOPENTYLOXY)CARBONYL]-D-LYSINE
3
EDO
20
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ATP A:900 , HOH A:996 , HOH A:998 , HOH A:1087 , HOH A:1088
BINDING SITE FOR RESIDUE MG A 500
02
AC2
SOFTWARE
GLU A:396 , SER A:399 , ATP A:900 , HOH A:1125 , HOH A:1158
BINDING SITE FOR RESIDUE MG A 501
03
AC3
SOFTWARE
ARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , MET A:344 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , GLY A:421 , GLY A:423 , ARG A:426 , MG A:500 , MG A:501 , CCL A:901 , EDO A:906 , HOH A:912 , HOH A:996 , HOH A:998 , HOH A:1087 , HOH A:1088 , HOH A:1125 , HOH A:1126 , HOH A:1128 , HOH A:1158 , HOH A:1160
BINDING SITE FOR RESIDUE ATP A 900
04
AC4
SOFTWARE
ASN A:241 , ARG A:439 , ALA A:440 , ASN A:448 , GLY A:449 , HOH A:960
BINDING SITE FOR RESIDUE EDO A 902
05
AC5
SOFTWARE
TYR A:242 , LEU A:246 , GLU A:249 , LYS A:431 , HIS A:432
BINDING SITE FOR RESIDUE EDO A 903
06
AC6
SOFTWARE
ASP A:373 , HIS A:392 , GLY A:393 , EDO A:904
BINDING SITE FOR RESIDUE EDO A 907
07
AC7
SOFTWARE
TYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , GLU A:444 , HOH A:983
BINDING SITE FOR RESIDUE EDO A 908
08
AC8
SOFTWARE
ASP A:373 , LYS A:375 , MET A:391 , HIS A:392 , GLY A:393 , EDO A:907
BINDING SITE FOR RESIDUE EDO A 904
09
AC9
SOFTWARE
SER A:225 , EDO A:910 , HOH A:975 , HOH A:980
BINDING SITE FOR RESIDUE EDO A 909
10
BC1
SOFTWARE
SER A:221 , LYS A:228 , EDO A:909
BINDING SITE FOR RESIDUE EDO A 910
11
BC2
SOFTWARE
ARG A:310 , ASP A:313 , GLY A:412 , ILE A:413 , ASP A:414 , LYS A:415
BINDING SITE FOR RESIDUE EDO A 905
12
BC3
SOFTWARE
LEU A:339 , GLU A:340 , GLU A:341 , ALA A:441 , HOH A:988
BINDING SITE FOR RESIDUE EDO A 911
13
BC4
SOFTWARE
GLU A:337 , HIS A:338 , ASP A:394 , GLU A:396 , ATP A:900
BINDING SITE FOR RESIDUE EDO A 906
14
BC5
SOFTWARE
ALA A:302 , LEU A:305 , TYR A:306 , ASN A:346 , SER A:399 , TRP A:417 , GLY A:419 , ALA A:420 , GLY A:421 , ATP A:900 , HOH A:1155 , HOH A:1157
BINDING SITE FOR RESIDUE CCL A 901
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2q7gA02 (A:240-454)
2a: CATH_2q7gA01 (A:188-239)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Methanosarcina mazei. Organism_taxid: 2209.
(4)
1a
2q7gA02
A:240-454
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(21)
Methanosarcina mazei. Organism_taxid: 2209.
(4)
2a
2q7gA01
A:188-239
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_tRNA_synt_2b_2q7gA01 (A:242-378)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2b
(25)
Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (Methanosarc
(7)
1a
tRNA-synt_2b-2q7gA01
A:242-378
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (57 KB)
Header - Asym.Unit
Biol.Unit 1 (99 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2Q7G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
